I have encountered a problem after using Tophat.
I started off with fasta file of my genome reference and a gff3 file of annotation reference. Nine sets of rnaseq data uploaded in my history.
I managed to run TopHat for the first two RNAseq data sets and was able to obtain all results from Tophat.
However for 5 datasets, there was a problem with the alignment summary, saying that an error occurred setting the metadata for this dataset. It was suggested to set it manually or retry auto-detection.

For the last two datasets, both alignment summary and insertions data from Tophat had this problem.
Do you reckon if there is a problem with the RNAseq data file? If so, will there be a way to repair RNAseq data file?
Could you please look into this for me and advice.

I've had a similar problem awhile back. You can try setting the metadata manually by clicking the pencil icon (edit attributes) next to your file that failed and then see if it can perform the downstream analysis steps (cufflinks etc).

From my experience it wont, and it was due to a miss-match with my gff3 file. Is there a specific reason you aren't running tophat using a genome already on galaxy?

Resetting the metadata is enough to create output that can be used with downstream tools. The jobs do not need to be re-run.

This has been reported a few times but we didn't have an example history with undeleted/uncorrected datasets present. But I was able to grab a quick copy of yours for our administrator to reference - he is troubleshooting right now.

Apologies for the confusion and thanks for reporting the problem!! Jen, Galaxy team